Integrated reference dataset comparison (Tyser & Zhai studies)
SC19181
Irene Rodriguez-Hernandez
February 2025
Integration of Tyser and Zhai datasets
We integrate the public datasets Tyser (1195 cells, Human) and Zhai CS8 (11629 cells, Macaca) following both the standard CCA integration approach and the RPCA approach.
CCA Integrated data
studies integrated
original annotation from each study
Clustering resolutions
Visualization of the different clustering resolutions of the integrated reference
Clustering the cells
integrated_snn_res.0.2
integrated_snn_res.0.4
integrated_snn_res.0.6
integrated_snn_res.0.8
integrated_snn_res.1
integrated_snn_res.1.2
integrated_snn_res.1.4
Dotplots of marker genes
integrated_snn_res.0.2
integrated_snn_res.0.4
integrated_snn_res.0.6
integrated_snn_res.0.8
integrated_snn_res.1
integrated_snn_res.1.2
integrated_snn_res.1.4
Cell proportions per cluster - original annotation
integrated_snn_res.0.2
integrated_snn_res.0.4
integrated_snn_res.0.6
integrated_snn_res.0.8
integrated_snn_res.1
integrated_snn_res.1.2
integrated_snn_res.1.4
RPCA Integrated data
studies integrated
original annotation from each study
Clustering resolutions
Visualization of the different clustering resolutions of the integrated reference
Clustering the cells
integrated_snn_res.0.2
integrated_snn_res.0.4
integrated_snn_res.0.6
integrated_snn_res.0.8
integrated_snn_res.1
integrated_snn_res.1.2
integrated_snn_res.1.4
Dotplots of marker genes
integrated_snn_res.0.2
integrated_snn_res.0.4
integrated_snn_res.0.6
integrated_snn_res.0.8
integrated_snn_res.1
integrated_snn_res.1.2
integrated_snn_res.1.4
Cell proportions per cluster - original annotation
integrated_snn_res.0.2
integrated_snn_res.0.4
integrated_snn_res.0.6
integrated_snn_res.0.8
integrated_snn_res.1
integrated_snn_res.1.2
integrated_snn_res.1.4
sessionInfo
## R version 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Rocky Linux 8.7 (Green Obsidian)
##
## Matrix products: default
## BLAS/LAPACK: /flask/apps/eb/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64/libflexiblas.so.3.0
##
## locale:
## [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
## [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] viridis_0.6.4 viridisLite_0.4.2 clustree_0.5.0 ggraph_2.1.0
## [5] cowplot_1.1.1 scales_1.2.1 ggpubr_0.6.0 patchwork_1.1.2
## [9] SeuratObject_4.1.3 Seurat_4.3.0.1 glue_1.6.2 DT_0.28
## [13] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2
## [17] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
## [21] ggplot2_3.4.2 tidyverse_2.0.0 here_1.0.1
##
## loaded via a namespace (and not attached):
## [1] readxl_1.4.3 backports_1.4.1 plyr_1.8.8
## [4] igraph_1.5.0.1 lazyeval_0.2.2 sp_2.0-0
## [7] splines_4.2.0 listenv_0.9.0 scattermore_1.2
## [10] digest_0.6.33 htmltools_0.5.5 fansi_1.0.4
## [13] checkmate_2.2.0 magrittr_2.0.3 tensor_1.5
## [16] cluster_2.1.4 ROCR_1.0-11 tzdb_0.4.0
## [19] globals_0.16.2 graphlayouts_1.0.0 matrixStats_1.0.0
## [22] timechange_0.2.0 spatstat.sparse_3.0-2 colorspace_2.1-0
## [25] ggrepel_0.9.3 xfun_0.39 jsonlite_1.8.7
## [28] progressr_0.13.0 spatstat.data_3.0-1 survival_3.5-5
## [31] zoo_1.8-12 polyclip_1.10-4 gtable_0.3.3
## [34] leiden_0.4.3 car_3.1-2 future.apply_1.11.0
## [37] abind_1.4-5 rstatix_0.7.2 spatstat.random_3.1-5
## [40] miniUI_0.1.1.1 Rcpp_1.0.11 xtable_1.8-4
## [43] reticulate_1.30 htmlwidgets_1.6.2 httr_1.4.6
## [46] RColorBrewer_1.1-3 ellipsis_0.3.2 ica_1.0-3
## [49] pkgconfig_2.0.3 farver_2.1.1 sass_0.4.7
## [52] uwot_0.1.16 deldir_1.0-9 utf8_1.2.3
## [55] labeling_0.4.2 tidyselect_1.2.0 rlang_1.1.1
## [58] reshape2_1.4.4 later_1.3.1 cellranger_1.1.0
## [61] munsell_0.5.0 tools_4.2.0 cachem_1.0.8
## [64] cli_3.6.1 generics_0.1.3 broom_1.0.5
## [67] ggridges_0.5.4 evaluate_0.21 fastmap_1.1.1
## [70] yaml_2.3.7 goftest_1.2-3 knitr_1.43
## [73] fitdistrplus_1.1-11 tidygraph_1.2.3 RANN_2.6.1
## [76] pbapply_1.7-2 future_1.33.0 nlme_3.1-162
## [79] mime_0.12 compiler_4.2.0 rstudioapi_0.15.0
## [82] plotly_4.10.1 png_0.1-8 ggsignif_0.6.4
## [85] spatstat.utils_3.0-3 tweenr_2.0.2 bslib_0.5.0
## [88] stringi_1.7.12 highr_0.10 lattice_0.21-8
## [91] Matrix_1.6-0 vctrs_0.6.3 pillar_1.9.0
## [94] lifecycle_1.0.3 spatstat.geom_3.2-4 lmtest_0.9-40
## [97] jquerylib_0.1.4 RcppAnnoy_0.0.21 data.table_1.14.8
## [100] irlba_2.3.5.1 httpuv_1.6.11 R6_2.5.1
## [103] promises_1.2.0.1 KernSmooth_2.23-22 gridExtra_2.3
## [106] parallelly_1.36.0 codetools_0.2-19 MASS_7.3-60
## [109] rprojroot_2.0.3 withr_2.5.0 sctransform_0.3.5
## [112] parallel_4.2.0 hms_1.1.3 grid_4.2.0
## [115] rmarkdown_2.23 carData_3.0-5 Rtsne_0.16
## [118] spatstat.explore_3.2-1 ggforce_0.4.1 shiny_1.7.4